The existence of a condition in the human body can often be detected and studied by detecting and studying certain protein-protein or cell-cell interactions that are organized in pathways associated with the condition. An example of an undesirable condition is cancer. As a cancerous tumor grows, the number of cancer cells increases. The human body has means to fight the cancer. Cytotoxic T-cells are a type of immune cells that are able to kill certain cancer cells. Cytotoxic T-cells are frequently present in greater numbers as the number of certain cancer cells increases due to the inflammatory nature of certain cancer types. The relationship between the density of cytotoxic T-cells and the density of such cancer cells can be said to be positively correlated. The actual biochemical communication channels between cells such as immune cells and cancer cells, and within cells such as from cell membrane to the cell nucleus with its DNA, are conceptually organized in pathways and represented in pathway diagrams. In general, multiple proteins in multiple states are involved in a pathway. Protein states may change by phosphorylation, methylation or conformational structure change. Most frequently the biochemical communication may be seen as a signaling pathway in which protein-protein interactions such as binding, or induced state change, are responsible for further processing the signal. Those signals may induce cell death or proliferation, activation of T-cells towards cytotoxic T-cells, or deadly release of toxic substances into the cancer cells by cytotoxic T-cells. Some cancer cells express certain proteins on their membranes that allow them to escape from cytotoxic T-cells and avoid the deadly release of cytotoxic substances by blocking the respective pathway in those T-cells. Drugs may, for example, be administered in an attempt to inhibit a step in a pathway so that another step in the pathway will be inhibited, or will be promoted. A drug may, for example, be administered to fight cancer by increasing the vulnerability of cancer cells to be killed by cytotoxic T-cells. Other drugs may work by causing cancer cells to be recognized as harmful by the immune system. Various drugs may work in various complex ways, and may have complex effects, on various pathways.
In order to study the efficacy of such a drug, it may be desirable to be able to detect changes in particular steps in a particular pathway. If, for example, the ultimate aim of a cancer treatment drug is to increase the vulnerability of cancer cells to be killed by cytotoxic T-cells, then a diagnostic system and tool that allows a physician or researcher to spatially measure the density of cytotoxic T-cells around cancer cells, which indicates specific immune-escape membrane proteins, would be useful. More generally, a diagnostic system and tool that allows a researcher to study relationships between any desired pair of proteins in a pathway would be useful in the development of medical treatments, drugs and diagnostics.